nf-core/genomeassembler
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Options controlling pipeline behavior
use reference genome
booleantrueskip assembly steps
booleanskip alignments during qc
booleanOptions for ONT reads
ONT reads available?
booleancollect ONT reads into a single file
booleanrun porechop on ONT reads
booleanread length for genomescope (ONT only)
integerrun jellyfish on ONT reads to compute k-mer distribution and estimate genome size
booleantruedump jellyfish output
booleankmer length to be used for jellyfish
integer21Options for HiFi reads
HiFi reads available?
booleanrun lima on HiFi reads?
booleanfile containing pacbio primers for trimming with lima
string^\S+\.fn?a(sta)?$Options controlling assembly
Assembler to use. Valid choices are: 'hifiasm', 'flye', 'flye_on_hifiasm' or hifiasm_on_hifiasm. flye_on_hifiasm will scaffold flye assembly (ont) on hifiasm (hifi) assembly using ragtag. hifiasm_on_hifiasm will scaffold hifiasm (ont) onto hifiasm (HiFi) using ragtag
stringexpected genome size, optional
integerflye mode
stringadditional args for flye
stringUse hifi and ONT reads with hifiasm --ul
booleanExtra arguments passed to hifiasm
stringOptions for short reads
Short reads available?
booleantrim short reads with trimgalore
booleantruekmer length for meryl / merqury
integer21Polishing options
Polish assembly with pilon? Requires short reads
booleanPolish assembly with medaka (ONT only)
booleanmodel to use with medaka
stringScaffolding options
Scaffold with longstitch?
booleanScaffolding with links?
booleanScaffold with ragtag (requires reference)?
booleanOptions for QC tools
Run merqury
booleantrueLong reads that should be used for QC when both ONT and HiFi reads are provided. Options are 'ONT' or 'HIFI'
stringRun BUSCO?
booleantruePath to busco db (optional)
stringBusco lineage to use
stringbrassicales_odb10Run quast
booleantrueOptions controlling annotation liftover
Lift-over annotations (requires reference)?
booleantrue